LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# Simple rigid body system

units           lj
atom_style      atomic

pair_style      lj/cut 2.5

read_data       data.rigid
Reading data file ...
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  81 atoms
  read_data CPU = 0.000 seconds

velocity        all create 100.0 4928459

# 2 chains of connected bodies

group           clump1 id <> 1 9
9 atoms in group clump1
group           clump2 id <> 9 18
10 atoms in group clump2
group           clump3 id <> 18 27
10 atoms in group clump3
group           clump4 id <> 27 36
10 atoms in group clump4
group           clump5 id <> 37 45
9 atoms in group clump5
group           clump6 id <> 45 54
10 atoms in group clump6
group           clump7 id <> 54 63
10 atoms in group clump7
group           clump8 id <> 63 72
10 atoms in group clump8
group           clump9 id <> 72 81
10 atoms in group clump9

#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
fix 1 all poems group clump1 clump2 clump3 clump4      clump5 clump6 clump7 clump8 clump9
2 clusters, 9 bodies, 7 joints, 81 atoms

neigh_modify    exclude group clump1 clump1
neigh_modify    exclude group clump2 clump2
neigh_modify    exclude group clump3 clump3
neigh_modify    exclude group clump4 clump4
neigh_modify    exclude group clump5 clump5
neigh_modify    exclude group clump6 clump6
neigh_modify    exclude group clump7 clump7
neigh_modify    exclude group clump8 clump8
neigh_modify    exclude group clump9 clump9

thermo          100

#dump           1 all atom 50 dump.rigid.poems2

#dump           2 all image 100 image.*.jpg type type #               axes yes 0.8 0.02 view 60 -30
#dump_modify    2 pad 5

#dump           3 all movie 100 movie.mpg type type #               axes yes 0.8 0.02 view 60 -30
#dump_modify    3 pad 5

timestep        0.0001
thermo          50
run             10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix poems command:

@Article{Mukherjee08,
 author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},
 title = {Substructured molecular dynamics using multibody dynamics algorithms},
 journal = {Intl.~J.~Non-linear Mechanics},
 year =    2008,
 volume =  43,
 pages =   {1045--1055}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 18 18 18
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.514 | 3.545 | 3.639 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    196.00047    3632.2347            0    3668.5311   -2.7403788 
      50    12774.759    1538.7382            0    3904.4344    18.086358 
     100    19803.641    237.21132            0    3904.5523   -3.1528278 
     150      20259.6    152.62072            0    3904.3985   -4.6173524 
     200    20705.978    69.977039            0    3904.4174    9.0928122 
     250    19552.211    283.50525            0     3904.285    15.670466 
     300    19266.324     333.5792            0    3901.4169    7.2119197 
     350    20738.325    63.738945            0    3904.1694    -23.03999 
     400    20616.682    86.082444            0    3903.9864   -13.783584 
     450    19831.326    230.13858            0    3902.6063   0.42074361 
     500    20365.825    131.47271            0    3902.9217   0.69215592 
     550    20794.102    52.163238            0    3902.9229    4.5895354 
     600    20853.873    40.899172            0    3902.7275    2.3593042 
     650    19255.802    336.29509            0    3902.1844    10.341742 
     700    18526.969    471.02462            0    3901.9448  -0.61898691 
     750    18960.662    391.26068            0    3902.4944     12.04731 
     800    20142.432    172.05197            0    3902.1319    4.6838632 
     850     19932.48    210.71175            0    3901.9118    3.4716031 
     900    20243.528    153.13972            0    3901.9411    3.6490762 
     950    20388.132    126.88722            0    3902.4671   -4.4518463 
    1000    20076.333    184.61915            0    3902.4586    -2.272315 
    1050    20859.506    39.696993            0    3902.5684      6.45166 
    1100    15284.661    1072.1908            0    3902.6836    21.194042 
    1150    19658.317    261.99809            0    3902.4272   -2.8744219 
    1200    20767.681    56.717095            0    3902.5839   -34.817444 
    1250    20625.583    82.586198            0    3902.1386    11.697328 
    1300    20690.013    71.006478            0    3902.4903    -29.29278 
    1350    20936.019    26.022786            0    3903.0634    1.0316025 
    1400     19753.56    244.81784            0    3902.8844    6.7138497 
    1450    15690.149    998.34213            0    3903.9252    48.124569 
    1500    20234.455    155.92516            0    3903.0465    13.172207 
    1550    20779.631    55.063019            0    3903.1428   -2.6390455 
    1600    20642.753    80.233821            0    3902.9659   -2.4688431 
    1650    18785.698    423.90364            0    3902.7365   -5.6466892 
    1700    20965.076    20.760451            0     3903.182  -0.45366172 
    1750    18935.412    396.95958            0    3903.5173    25.913174 
    1800    20581.554    91.757912            0    3903.1567    3.8218442 
    1850    20616.949    85.184789            0    3903.1382    4.1907933 
    1900    16601.896    828.43849            0    3902.8638  -0.49468175 
    1950    20175.564    166.52646            0    3902.7421    5.6035728 
    2000    20262.525    150.28224            0    3902.6017   -1.1967705 
    2050    20168.994    167.65314            0    3902.6521  -0.80723928 
    2100    19810.955    232.96524            0    3901.6605    3.1936531 
    2150    20667.232    75.645145            0    3902.9103   0.54812734 
    2200    19863.772    224.34646            0    3902.8228    7.9294465 
    2250    18808.943     419.2084            0    3902.3461    14.344526 
    2300    20573.665    92.761842            0    3902.6999   -6.7671703 
    2350    19075.104    369.95414            0    3902.3809   -9.5353568 
    2400    20273.873    148.53775            0    3902.9586     -1.93796 
    2450    20087.769    182.30216            0    3902.2593     2.131796 
    2500    20711.602    67.530554            0    3903.0124    2.6280244 
    2550    19971.224    204.75926            0     3903.134    3.1760522 
    2600    20620.084    85.027145            0    3903.5612  -0.92888063 
    2650    19737.546    248.65474            0    3903.7559   -3.3218688 
    2700    20650.724    79.522243            0    3903.7303   -7.5918025 
    2750    19863.245     225.2505            0    3903.6292    9.2140221 
    2800    18992.457    386.73547            0    3903.8572    2.6244537 
    2850    18703.899    440.48356            0    3904.1685    14.561348 
    2900    17939.805    581.74599            0     3903.932   -8.0863089 
    2950    20867.516     39.38186            0    3903.7367    3.0985423 
    3000    19767.994     242.8847            0    3903.6243    1.5943109 
    3050    20397.448    126.31591            0    3903.6212  -0.14982775 
    3100    20978.114    19.126395            0    3903.9623   -9.6797253 
    3150    18303.556     513.8514            0    3903.3989    4.5940322 
    3200    19156.505    356.46608            0    3903.9671    10.071308 
    3250    17484.205    666.52199            0    3904.3377   -4.1641768 
    3300     18069.94    557.75947            0    3904.0447    11.868707 
    3350    20855.645    41.964632            0    3904.1212    5.4186293 
    3400    18011.986    568.76255            0    3904.3155    25.262783 
    3450     18669.69    446.92755            0    3904.2776    -4.194499 
    3500    20248.799    154.22147            0    3903.9991    3.9211572 
    3550    20226.024    158.64726            0    3904.2072    1.5299114 
    3600     20267.02    151.25631            0    3904.4082   -8.9821729 
    3650    20522.946    103.65382            0    3904.1994   -14.433796 
    3700    20892.319    35.294614            0    3904.2426   -21.264596 
    3750    19942.202    211.02993            0    3904.0304   -1.6428817 
    3800    20421.678    122.08118            0    3903.8734    1.7137935 
    3850     17899.53    588.82593            0    3903.5536   -24.450276 
    3900    20721.119    66.486999            0    3903.7312   -7.1772088 
    3950    20946.484    24.799445            0     3903.778   -0.4028037 
    4000    20985.362    17.608355            0    3903.7865    4.7522266 
    4050    19969.779    205.46466            0    3903.5719    18.941639 
    4100    20479.578    110.56561            0      3903.08    2.3715952 
    4150    18110.701    549.53348            0     3903.367     1.133321 
    4200    19321.098    325.58216            0    3903.5634   -3.7574942 
    4250    20734.436     63.87616            0    3903.5865   0.48350623 
    4300    19446.823     302.1727            0    3903.4362    4.0462392 
    4350    20494.669     108.1918            0     3903.501    2.9789077 
    4400    20379.244    129.61413            0    3903.5482    4.0881089 
    4450    19710.564     253.4251            0    3903.5295    5.3334683 
    4500    20744.753    61.785082            0     3903.406    4.0015409 
    4550    19948.024    208.76984            0    3902.8484     2.705423 
    4600    18367.368    502.69569            0    3904.0602    21.476471 
    4650    20559.367    96.133242            0    3903.4234    2.2549454 
    4700    20940.135    25.547808            0    3903.3505   -8.9042666 
    4750    20128.703    175.82088            0    3903.3584   -8.1450176 
    4800     20632.27    82.543887            0    3903.3347  -0.55649542 
    4850    19864.539    224.63792            0    3903.2563    7.1553461 
    4900    19332.037    323.15561            0    3903.1625    17.020214 
    4950    19055.575    373.68069            0    3902.4908    10.149457 
    5000    20219.484    159.21383            0    3903.5627    3.1806346 
    5050    17557.761    652.32864            0    3903.7659    10.733736 
    5100    20615.337    85.795304            0    3903.4503   -3.6035636 
    5150    20759.853    59.155843            0     3903.573    2.0152286 
    5200    20082.007    184.39375            0    3903.2839   -5.3745109 
    5250    18689.521    442.59842            0    3903.6208   -9.8911164 
    5300    20038.496    192.34221            0    3903.1749   -2.1437039 
    5350    19897.455    218.70142            0    3903.4154   0.64582116 
    5400    18732.385    434.21543            0    3903.1755     12.98676 
    5450    19831.487    230.79099            0    3903.2886    11.439958 
    5500     20079.89     184.6953            0    3903.1935    4.0906279 
    5550    20453.497    115.47128            0    3903.1559    7.8844436 
    5600    16673.041    815.52661            0    3903.1267    -20.17797 
    5650    19691.378     256.6412            0    3903.1928    3.7103317 
    5700    20345.743    135.29997            0    3903.0302    5.6373816 
    5750    20769.613    56.906603            0    3903.1312   -17.564762 
    5800    20713.369     67.38314            0    3903.1922    -5.340631 
    5850    20799.947    51.348865            0    3903.1909   -2.7827653 
    5900    19581.933    273.51588            0    3899.7997    12.347375 
    5950    20444.438      116.909            0    3902.9161  -0.74896654 
    6000    18970.948    389.99664            0    3903.1352    26.642912 
    6050    19414.753    307.13217            0    3902.4568     25.86316 
    6100    20780.042    54.586474            0    3902.7424    1.5387425 
    6150    20885.872    35.091585            0    3902.8456    -8.251884 
    6200     19825.81    231.40943            0    3902.8558    6.7196589 
    6250    20578.278    92.255994            0    3903.0481   -5.9647091 
    6300     20093.43     181.8699            0    3902.8754   -9.9906069 
    6350    20605.294    87.180289            0    3902.9755   -3.5643876 
    6400    19737.257    247.84828            0    3902.8958   -4.2783347 
    6450    19884.717    220.81633            0    3903.1714    3.8758905 
    6500    18719.372    436.94802            0    3903.4984    1.7865904 
    6550    20096.883    181.63346            0    3903.2784     2.395512 
    6600    20888.673    35.003062            0    3903.2758    2.7728947 
    6650     20437.85    118.16373            0    3902.9507    8.1456757 
    6700    19241.051    339.73065            0    3902.8882    13.740454 
    6750    20407.542    123.94326            0    3903.1177    7.6285942 
    6800    20536.785    99.976706            0    3903.0851    8.3496632 
    6850    20625.328    83.579677            0    3903.0849    6.5074992 
    6900     20705.37    68.944625            0    3903.2724    3.1905177 
    6950    18872.424    408.67134            0    3903.5647    6.2638845 
    7000    20072.762    186.18051            0    3903.3586   -22.780407 
    7050    20461.879    114.07495            0    3903.3117   -11.495523 
    7100    19811.566    234.50237            0    3903.3108    1.1212695 
    7150    20742.918    61.884088            0    3903.1651   -3.7907508 
    7200    20911.192    30.599903            0    3903.0429   -7.0262304 
    7250    20879.755     36.30274            0    3902.9241   -5.8018787 
    7300     20682.32    72.703261            0    3902.7626   -3.3446789 
    7350    19401.046    309.70672            0     3902.493    3.4836528 
    7400    20220.542    157.83897            0    3902.3838    2.3400031 
    7450    17691.193    625.47764            0    3901.6244    25.239568 
    7500    19745.294    245.02566            0    3901.5615    5.3622843 
    7550    19685.719    256.70983            0    3902.2133    3.4560563 
    7600    18830.192    415.10021            0    3902.1727  -0.10282681 
    7650    19613.136    270.18979            0    3902.2521    8.2241536 
    7700    20989.015    15.636879            0    3902.4915    1.2955204 
    7750    20301.583    142.90625            0    3902.4586   0.12548373 
    7800    18360.147    502.50342            0    3902.5307    17.117272 
    7850    20796.478    51.032537            0    3902.2321   -3.0993883 
    7900    20284.267    145.64296            0    3901.9887   -1.2682383 
    7950    20280.983    146.13471            0    3901.8723    3.5999841 
    8000    20915.869    28.730821            0    3902.0399    2.4987291 
    8050    20745.162     60.19981            0    3901.8964    4.0643481 
    8100    20509.039    103.70462            0    3901.6748    1.0771863 
    8150     20212.97    158.64893            0    3901.7916    3.0000215 
    8200    20323.463    138.25912            0    3901.8634   -1.2802945 
    8250    19997.284    198.37183            0    3901.5727   -2.6431964 
    8300    20138.402    171.75824            0     3901.092    1.7669897 
    8350    20367.568    130.22531            0    3901.9972   -1.2153731 
    8400    19945.534    208.35675            0    3901.9741    1.6021151 
    8450    20112.534    177.18642            0    3901.7298    2.2413008 
    8500      20686.7    71.116816            0    3901.9873    2.2888545 
    8550     18081.94    553.83586            0    3902.3432    7.8257937 
    8600    18320.081    505.67086            0    3898.2784    16.554878 
    8650    20235.305    154.43021            0     3901.709    3.1740823 
    8700    20355.413    132.22512            0     3901.746    4.3436482 
    8750    20087.188    182.11349            0    3901.9631    10.422134 
    8800    20400.795    124.09819            0    3902.0232    2.1179177 
    8850    20678.731    72.825797            0    3902.2204   -3.4491441 
    8900    20372.643     129.5072            0    3902.2189   -8.2166415 
    8950    20851.731    40.899364            0     3902.331   -5.8382839 
    9000    20318.076    139.61775            0    3902.2243   -4.1960802 
    9050    16879.415    776.53739            0    3902.3549   -14.429475 
    9100    19135.149    358.68223            0    3902.2284    -15.50479 
    9150    20689.556    70.939656            0     3902.339   -2.9876179 
    9200    19949.801    207.54882            0    3901.9564    6.4259245 
    9250    20207.027     160.2813            0    3902.3233    1.7402195 
    9300    20030.005    192.99466            0    3902.2548     5.300728 
    9350    19795.291    236.24003            0    3902.0347    5.8677745 
    9400    18232.093    526.18752            0     3902.501    19.344893 
    9450    18789.641    422.30568            0    3901.8687   -7.5185247 
    9500    16332.599    874.10423            0    3898.6597    16.241378 
    9550    18572.572    462.19972            0    3901.5649   -10.777359 
    9600    19859.645    223.32209            0    3901.0341   0.89631957 
    9650    19092.741    365.35768            0    3901.0504    6.7830005 
    9700    18391.154    495.72792            0    3901.4972    6.0683847 
    9750    17790.092    608.60997            0    3903.0714    8.2090184 
    9800    17681.783    628.99951            0    3903.4038    14.231747 
    9850    17804.412    605.54067            0     3902.654    22.308453 
    9900    19134.472    359.37911            0    3902.7999    8.5633158 
    9950    20099.055    180.28604            0    3902.3332    4.7905855 
   10000    20035.447    192.30744            0    3902.5754    1.8299201 
Loop time of 2.31994 on 4 procs for 10000 steps with 81 atoms

Performance: 37242.315 tau/day, 4310.453 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0052789  | 0.014781   | 0.038634   |  11.4 |  0.64
Neigh   | 0.0081228  | 0.016514   | 0.033404   |   7.7 |  0.71
Comm    | 0.12269    | 0.13668    | 0.14951    |   3.1 |  5.89
Output  | 0.0034489  | 0.0039413  | 0.0050811  |   1.1 |  0.17
Modify  | 2.1036     | 2.1312     | 2.1509     |   1.2 | 91.86
Other   |            | 0.01685    |            |       |  0.73

Nlocal:          20.25 ave          36 max           0 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost:          35.25 ave          47 max          24 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs:          137.5 ave         252 max           0 min
Histogram: 1 0 0 1 0 0 0 0 1 1

Total # of neighbors = 550
Ave neighs/atom = 6.7901235
Neighbor list builds = 994
Dangerous builds = 956
Total wall time: 0:00:02
